3TDN | pdb_00003tdn

Computationally designed two-fold symmetric Tim-barrel protein, FLR

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		COMPUTATIONAL MODEL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	4.2	291	20% PEG 1000, 0.1M SODIUM CITRATE, 0.1 M AMMONIUM CHLORIDE, pH 4.2, Microbatch, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.222	α = 90
b = 67.222	β = 90
c = 124.658	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2009-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 12.3.1		ALS	12.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.4	50	98	0.072	19.35	9.7		63971			21

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.45	96.9		0.683	3.01	9.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	COMPUTATIONAL MODEL	1.4	42.5	60459	3264	97.9	0.159	0.157	0.17	0.193	0.2	RANDOM	21.27

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-4.31			-4.31		8.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.021
r_dihedral_angle_4_deg	18.903
r_dihedral_angle_3_deg	12.629
r_scangle_it	7.332
r_dihedral_angle_1_deg	5.463
r_scbond_it	5.273
r_mcangle_it	4.311
r_mcbond_it	2.916
r_rigid_bond_restr	2.353
r_angle_refined_deg	1.814
r_angle_other_deg	1.096
r_mcbond_other	0.981
r_chiral_restr	0.146
r_bond_refined_d	0.023
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2719
Nucleic Acid Atoms
Solvent Atoms	259
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling